Abu Suleiman was working methodically to wrap the body of a seven-year-old girl in a white shroud. He didn't flinch as a volley of mortar bombs crashed down only a street away. He has been preparing the dead for burial since the start of the uprising. Last week he had his busiest day.

Carefully, he folded over the white cloth to cover the girl's curly chestnut hair, matted with blood. He did not clean it off. "If they are killed by a bomb or a bullet, we don't wash their martyrs' blood," he said. He wrote the girl's name on the shroud, Nuha al-Manal.

"Of course, it a very difficult job," he added. "Among those I prepared for burial were my son, my son-in-law, my nephew, my neighbour, my friend. But it has to be done. I feel I owe these people something. The least I can do is to wrap them in their shrouds."

Such long lists of the dead were common in the Baba Amr quarter of Homs. Abu Sufyan had lost a brother, a nephew, an uncle, and, most recently, his mother. A warm and generous man – we had stayed in his house last November – he had become prone to explosions of rage.

He shouted at a hysterical woman in the makeshift hospital. Her son's foot had been neatly severed by a mortar. Someone was holding it, wrapped in a bloody keffiyeh. She was ululating, clutching her face. "Give us guns so we can defend ourselves," she wailed, piercingly. Abu Sufyan had no patience with this. "We've had a hundred martyrs already today," he bellowed. "Get out so the doctors can work."

Most of the casualties we saw were civilians and many were children. An 11-year-old boy was brought in. Most of his face had been torn off in an explosion. Everything below the mid-point of his nose was gone, bloody shreds hanging over a hole where his jaw and mouth had been.

Bombs were continually falling outside. People were screaming in the corridor. The boy was still conscious. We caught a glimpse of eyes wide with shock before the nurses pulled a screen across. We decided to try to find a surgeon outside Syria who could reconstruct his face, but the boy died of his wounds the following day.

When the first shells and mortars began to fall, men came out on to the streets with defiant shouts of "God is great". We drove with Jedi, a local cameraman who had been a vegetable seller before the revolution. (You may have seen his shaky images of shells falling, uploaded to YouTube.)

He parked his van at a crossroads to show us the smoking hole from a mortar impact in a mosque opposite.

Me: "That's very interesting, but we should go now."

Jedi: "No, we're safe."

Me, with strained calm: "But perhaps it would be better to get under hard cover."

Jedi: "No, they can't hit here."

We went back and forth for an agonisingly long minute before Jedi U-turned, parked, and we got into a doorway. Then, another mortar hit, covering the junction in a billowing cloud of black smoke.

He had seemed strangely disconnected from the danger, but they were used to being attacked: Baba Amr had been under siege for months. Jedi snapped on the third day after hundreds of shells, mortars and rockets had fallen. He walked back and forth shouting: "The army is about to use chemical weapons. They're already sending in ground troops." Neither was true. Under the constant shelling, people were becoming hysterical.

State television denied there was a bombardment. It told the inventive lie that residents were setting fire to rubbish on their roofs to give the impression of an attack. The official media also said that most of the violence was caused by the rebel fighters of the Free Syrian Army – "terrorists", "criminal gangs" or "agents of Israel" in the language of official spokesmen.

Free Syrian Army fighters in Baba Amr had attacked government sniper positions, losing two men, their commander, Captain Mohammed Idris, said. He didn't think that the rebel fighters' growing strength had provoked the government into attacking, they were doing that anyway, he said. "The regime can't get to us, so it retaliates against civilians instead."

Another Free Syrian Army officer, who had defected only a week ago, said morale within the security forces had collapsed. He had been a full colonel and – like the other defectors – still wore his uniform. "They know they're killing civilians and they want this bloodbath to stop," he said.

The rebels have to hope that the Syrian army will crumble from inside. What else can they do? They have Kalashnikovs; the regime has tanks.

We were smuggled into Syria and then into Homs by the rebels. Although it has a military council and a spokesman in Turkey, the "Free Army" is not a single organisation with a coherent command structure. It is more a name used by local militias. Arriving just over the border from Lebanon, we found two separate, rival Free Army groups with commanders who did not much like each other.

We followed one of the groups into an attack against an army base. The attack was big, more than 60 men, all of whom had defected from the Syrian forces. By contrast with, say, the fighters in Libya, they were trained, disciplined and followed a plan of attack. Of course, that plan failed. After an hour of firing on the base, they fled when the government troops brought up heavy weapons.

As they retreated through the village nearby, a man came up to them shaking with anger.

"I support the revolution," he screamed, "but I am here with my wife and children. If you are going to attack the base, then attack it properly. Destroy it. Now the soldiers will come here and we will suffer."

Afterwards one of the Free Army fighters showed me a video he had taken in December. A dozen men in Syrian army uniform were lined up facing a wall. They arms were raised; one turns to the camera looking petrified. Some were still bleeding. Despite their army uniforms, he said their ID cards showed they were Shabiha, or "ghosts", the hated government paramilitary force.

"We killed them," he told me.

"You killed your prisoners?"

"Yes, of course, that is the policy for Shabiha."

I checked with an officer. While soldiers were released, he said, members of the Shabiha were executed after a hearing before a panel of Free Syrian Army military judges. To explain, they showed me film taken from the mobile phone of a captured Shabiha. Prisoners lay face down on the ground, hands tied behind their backs. One by one, their heads were cut off. The man wielding the knife said, tauntingly, to the first: "This for freedom." As his victim's neck opened, he went on: "This is for our martyrs. And this is for collaborating with Israel."

In Homs, after we left, there were reports from human rights activists that the Shabiha, going house to house, had murdered three families, men, women and children. To most of the Free Syrian Army fighters, "executing" the Shabiha seems only just.

Such things will give western governments pause as they decide whether, or increasingly how, to help the rebels. If they help the rebels, will they fuel a civil war or, worse, a sectarian civil war? If they do not, how can the killing in Homs, and elsewhere, be stopped? In Homs, people seem to have given up hope. A mother told me how her two young children would follow her around the house, crying at each impact. "All we have is God," she said. "May he bring his vengeance down on Bashar [al-Assad, the Syrian president]."

We slipped out of the city during a pause in the bombardment. Our cameraman, Fred Scott, had filmed the burial of the little girl, Nuha al-Manal. It took place at night since, they said, funerals were regularly attacked. Even so, it was too dangerous for relatives of the child to attend.

A volunteer ran, stumbling, across the graveyard, with the small body grasped in his arms. There was no time to offer prayers. There was only the rapid scrape of shovels and a burst of gunfire in their direction as she was hurriedly put in the ground. There will be many more such lonely and desperate burials in Homs.

Paul Wood is a BBC foreign correspondent. He went into Syria with a BBC cameraman, Fred Scott, and a medic, Kevin Sweeney.